Required for DOCKing

• MPICH Library: library required to compile MPI function
• Cygwin: Linux-like environment required to run Windows version of DOCK
• g77 3.4: fortran compiler required to run accessory programs on MacIntosh
• dms: computes molecular surface of molecule

Other Useful Programs

• babel: interconverts a number of file formats currently used in molecular modeling

• Sybyl: visualization and computation of chemical properties
• Moe: visualization and computation of chemical properties
• Quac Pac: pKa and tautomer enumeration in order to get correct protonation states and partial charge calculation (Open Eye)
• Chimera: UCSF
• Molecular Visualization Freeware (Protein Explorer, RasMol, and Chime): U Mass, Amherst
• Vida: Open Eye
• PyMol: DeLano Scientific

• AMBER: Molecular Dynamics simulation package
• MORDOR: Fully flexible docking package

Discussion Forums

• www.docking.org: docking community blog hosted by the Shoichet Group